def __init__(self, name, by="symbol"):
super().__init__("gene")
assert type(name) == str, "name must be string"
if by not in ["name", "symbol", "entrez", "ensembl"]:
raise ValueError(
"""by must be in ["name", "symbol", "entrez", "ensembl"] """)
by_dict = {
"name": "Approved name",
"entrez": "ENTREZ ID",
"ensembl": "Ensembl ID"
}
try:
info = data.genes.loc[name]
except (ValueError, KeyError):
info = data.genes.loc[data.genes[by_dict[by]] == name].iloc[0]
self.symbol = info.name
self.name = info["Approved name"]
self.entrez = info["ENTREZ ID"]
self.ensembl = info["Ensembl ID"]
self._grabber = grabber.Grabber("gene", self.symbol, self._axis)
self._subset_handler = SubsetHandler()
def __init__(self, lines, all_except=False):
super().__init__("canc")
assert isinstance(lines, MutableSequence), "Must be list or array-like"
if not all_except:
try:
info = data.cell_lines.loc[lines]
except KeyError:
info = data.cell_lines.loc[
data.cell_lines.cell_line_name.isin(lines), ]
except KeyError:
info = data.cell_lines.loc[
data.cell_lines.CCLE_Name.isin(lines), ]
except IndexError:
raise ValueError(
"Cannot Instantiate CellLine object with {}".format(lines))
else:
info = data.cell_lines[~lines]
self.disease = info["lineage"].unique()
self.subtypes = info["lineage_subtype"].unique()
self.names = list(info.cell_line_name)
self.ccle_names = list(info.CCLE_Name)
self.depmap_ids = list(info.index)
self.genders = info.sex.unique()
self.sources = info.source.unique()
self._info = info
self._string_meth = lambda x, y: x[y]
self._grabber = grabber.Grabber("canc", self.depmap_ids, self._axis)
self._subset_handler = SubsetHandler()
def __init__(self,
disease,
subtype=None,
gender=None,
source=None,
all_except=False):
super().__init__("canc")
if subtype is None and all_except is False:
info = data.cell_lines.loc[data.cell_lines["primary_disease"].isin(
[disease])]
elif subtype is None and all_except is True:
info = data.cell_lines.loc[~data.cell_lines["primary_disease"].
isin([disease])]
disease = "All Except {}".format(disease)
else:
info = data.cell_lines.loc[data.cell_lines["lineage_subtype"] ==
subtype, ]
if gender:
info = info.loc[info.sex == gender]
if source:
info = info.loc[info.source == source]
self.disease = disease
self.depmap_ids = list(info.index)
self.names = list(info.cell_line_name)
self.ccle_names = list(info.CCLE_Name)
self.subtypes = info["Subtype"].unique()
self.sexes = info.sex.unique()
self.sources = info.source.unique()
self._info = info
self._string_meth = lambda x, y: x.loc[y]
self._grabber = grabber.Grabber("canc", self.depmap_ids, self._axis)
self._subset_handler = SubsetHandler()
def __init__(self, cellline):
super().__init__("line")
assert type(cellline) == str, "cellline must be string"
try:
info = data.cell_lines.loc[cellline]
except KeyError:
info = data.cell_lines.loc[data.cell_lines.cell_line_name ==
cellline].iloc[0]
except KeyError:
info = data.cell_lines.loc[data.cell_lines.CCLE_Name ==
cellline].iloc[0]
except IndexError:
raise ValueError(
"Cannot Instantiate CellLine object with {}".format(cellline))
self.depmap_id = info.name
self.ccle_name = info.CCLE_Name
self.name = info["stripped_cell_line_name"]
self.tissue = info.lineage
self.aliases = info.alias
self.cosmic_id = info.COSMICID
self.sanger_id = info["Sanger_Model_ID"]
self.sex = info.sex
self.source = info.source
self.lineage = info["lineage"]
self.subtype = info["lineage_subtype"]
self._grabber = grabber.Grabber("line", self.depmap_id, self._axis)
self._subset_handler = SubsetHandler()
def __init__(self, genes, name=None):
super().__init__("org")
self.genes = genes
locs = data.locations.loc[data.locations.gene.isin(genes)]
self._string_meth = lambda x, y: x[y]
self.name = name
self._grabber = grabber.Grabber("org", self.genes, self._axis)
self._subset_handler = SubsetHandler()
def __init__(self, organelle, min_conf=3):
super().__init__("org")
self.location = organelle
self.conf = min_conf
locs = data.locations.loc[data.locations.location == organelle]
self.genes_and_conf = locs.loc[locs.confidence >= min_conf, :].reindex(
["gene", "confidence"], axis=1)
self.genes = list(self.genes_and_conf.gene)
self._string_meth = lambda x, y: x[y]
self._grabber = grabber.Grabber("org", self.genes, self._axis)
self._subset_handler = SubsetHandler()